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Anopheles gambiae vs Aedes aegypti (LVP_AGWG) LastZ results

Anopheles gambiae (Anopheles gambiae, AgamP4) and Aedes aegypti (LVP_AGWG) (Aedes aegypti, AaegL5) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Metazoa release 99. Anopheles gambiae was used as the reference species. After running LastZ, the raw LastZ alignment blocks were chained according to their location in both genomes. During the final netting process, the best sub-chain was chosen in each region on the reference species.

Configuration parameters

ParameterValue
Gap open penalty (O)400
Gap extend penalty (E)30
HSP threshold (K)
Threshold for gapped extension (L)3000
Threshold for alignments between gapped alignment blocks (H)2200
Masking count (M)
Seed and Transition value (T)1
Scoring matrix (Q)
Default:
     A    C    G    T
    91 -114  -31 -123
  -114  100 -125  -31
   -31 -125  100 -114
  -123  -31 -114   91

Chunking parameters

ParameterAnopheles gambiaeAedes aegypti (LVP_AGWG)
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size010,100,000
Masking options{default_soft_masking => 1}{default_soft_masking => 1}

Statistics over 63,333 alignment blocks

Genome coverage (bp) Coding exon coverage (bp)
Anopheles gambiae

Uncovered: 258,789,954 out of 281,378,673
Covered: 22,588,719 out of 281,378,673

Uncovered: 5,221,254 out of 22,369,942
Matches: 11,737,150 out of 22,369,942
Mismatches: 4,690,596 out of 22,369,942
Insertions: 720,942 out of 22,369,942
Identity over aligned base-pairs: 68.4%

Aedes aegypti (LVP_AGWG)

Uncovered: 1,255,371,506 out of 1,278,732,104
Covered: 23,360,598 out of 1,278,732,104

Uncovered: 6,539,813 out of 24,304,798
Matches: 12,291,418 out of 24,304,798
Mismatches: 5,128,748 out of 24,304,798
Insertions: 344,819 out of 24,304,798
Identity over aligned base-pairs: 69.2%

Block size distribution

Size range All 63,333 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
161
940.0 bp
10 bp - 100 bp
11,159
735.1 kb
5,363
367.9 kb
100 bp - 1 kb
45,722
16.2 Mb
21,448
8.0 Mb
1 kb - 10 kb
6,277
10.6 Mb
7,524
17.1 Mb
10 kb - 100 kb
14
203.9 kb
142
2.2 Mb